An efficient solution for resolving iTRAQ and TMT channel cross‐talk

Isobaric tagging reagents such as isobaric tag for relative and absolute quantitation (iTRAQ) and tandem mass tag (TMT) typically have isotopic impurities that cause significant cross‐talk between channels. Here, we present an efficient solution to compensate for channel cross‐talk using linear algebra and find that it is between 20× and 120× faster than previous methods. We also find that the effects of channel cross‐talk are as important to manage as the effects of ratio compression because of precursor impurities, and we have released an open‐source tool to perform both types of calculations.     

Peptide and protein quantification using iTRAQ with electron transfer dissociation

Electron transfer dissociation (ETD) has become increasingly used in proteomic analyses due to its complementarity to collision-activated dissociation (CAD) and its ability to sequence peptides with post-translation modifications (PTMs). It was previously unknown, however, whether ETD would be compatible with a commonly employed quantification technique, isobaric tags for relative and absolute quantification (iTRAQ), since the fragmentation mechanisms and pathways of ETD differ significantly from CAD. We demonstrate here that ETD of iTRAQ labeled peptides produces c- and z -type fragment ions as well as reporter ions that are unique from those produced by CAD. Exact molecular formulas of product ions were determined by ETD fragmentation of iTRAQ-labeled synthetic peptides followed by high mass accuracy orbitrap mass analysis. These experiments revealed that ETD cleavage of the N-C(alpha) bond of the iTRAQ tag results in fragment ions that could be used for quantification. Synthetic peptide work demonstrates that these fragment ions provide up to three channels of quantification and that the quality is similar to that provided by beam-type CAD. Protein standards were used to evaluate peptide and protein quantification of iTRAQ labeling in conjunction with ETD, beam-type CAD, and pulsed Q dissociation (PQD) on a hybrid ion trap-orbitrap mass spectrometer. For reporter ion intensities above a certain threshold all three strategies provided reliable peptide quantification (average error < 10%). Approximately 36%, 8%, and 16% of scans identified fall below this threshold for ETD, HCD, and PQD, respectively. At the protein level, average errors were 2.3%, 1.7%, and 3.6% for ETD, HCD, and PQD, respectively.     

Novel method to investigate protein carbonylation by iTRAQ strategy

This paper reports a novel methodology for relative quantitative analysis of carbonylation sites in proteins by exploiting a new isobaric tag for relative and absolute quantitation (iTRAQ) derivative, iTRAQ hydrazide (iTRAQH), and the analytical power of linear ion trap instruments (QqLIT). Because of its operational simplicity, avoiding time-consuming enrichment procedures, this new strategy seems to be well suited for quantitative large-scale proteomic profiling of carbonylation.     

Quaternary ammonium isobaric tag for a relative and absolute quantification of peptides

Isobaric labeling quantification of peptides has become a method of choice for mass spectrometry‐based proteomics studies. However, despite of wide variety of commercially available isobaric tags, none of the currently available methods offers significant improvement of sensitivity of detection during MS experiment. Recently, many strategies were applied to increase the ionization efficiency of peptides involving chemical modifications introducing quaternary ammonium fixed charge. Here, we present a novel quaternary ammonium–based isobaric tag for relative and absolute quantification of peptides (QAS‐iTRAQ 2‐plex). Upon collisional activation, the new stable benzylic‐type cationic reporter ion is liberated from the tag. Deuterium atoms were used to offset the differential masses of a reporter group. We tested the applicability of QAS‐iTRAQ 2‐plex reagent on a series of model peptides as well as bovine serum albumin tryptic digest. Obtained results suggest usefulness of this isobaric ionization tag for relative and absolute quantification of peptides.     

Enhanced Performance of Pulsed Q Collision Induced Dissociation-Based Peptide Identification on a Dual-Pressure Linear Ion Trap

Pulsed Q collision induced dissociation (PQD) was introduced for isobaric tag quantification on linear ion traps to circumvent the problem of the low-mass cut-off for collision induced dissociation (CID). Unfortunately, fragmentation efficiency is compromised and PQD has found limited use for identification as well as quantification. We demonstrate that PQD has a comparable peptide identification performance to CID on dual-pressure linear ion traps, opening the potential for wider use of isobaric tag quantification on this new generation of linear ion traps.     

Click chemistry facilitates formation of reporter ions and simplified synthesis of amine-reactive multiplexed isobaric tags for protein quantification

We report the development of novel reagents for cell-level protein quantification, referred to as Caltech isobaric tags (CITs), which offer several advantages in comparison with other isobaric tags (e.g., iTRAQ and TMT). Click chemistry, copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC), is applied to generate a gas-phase cleavable linker suitable for the formation of reporter ions. Upon collisional activation, the 1,2,3-triazole ring constructed by CuAAC participates in a nucleophilic displacement reaction forming a six-membered ring and releasing a stable cationic reporter ion. To investigate its utility in peptide mass spectrometry, the energetics of the observed fragmentation pathway are examined by density functional theory. When this functional group is covalently attached to a target peptide, it is found that the nucleophilic displacement occurs in competition with formation of b- and y-type backbone fragment ions regardless of the amino acid side chains present in the parent bioconjugate, confirming that calculated reaction energetics of reporter ion formation are similar to those of backbone fragmentations. Based on these results, we apply this selective fragmentation pathway for the development of CIT reagents. For demonstration purposes, duplex CIT reagent is prepared using a single isotope-coded precursor, allyl-d(5)-bromide, with reporter ions appearing at m/z 164 and 169. Isotope-coded allyl azides for the construction of the reporter ion group can be prepared from halogenated alkyl groups which are also employed for the mass balance group via N-alkylation, reducing the cost and effort for synthesis of isobaric pairs. Owing to their modular designs, an unlimited number of isobaric combinations of CIT reagents are, in principle, possible. The reporter ion mass can be easily tuned to avoid overlapping with common peptide MS/MS fragments as well as the low mass cutoff problems inherent in ion trap mass spectrometers. The applicability of the CIT reagent is tested with several model systems involving protein mixtures and cellular systems.     

Targeted data acquisition for improved reproducibility and robustness of proteomic mass spectrometry assays

Quantitative mass spectrometry-based proteomic assays often suffer from a lack of robustness and reproducibility. We here describe a targeted mass spectrometric data acquisition strategy for affinity enriched subproteomes—in our case the kinome—that enables a substantially improved reproducibility of detection, and improved quantification via isobaric tags. Inclusion mass lists containing m/z, charge state, and retention time were created based on a set of 80 shotgun-type experiments performed under identical experimental conditions. For each target protein, peptides were selected according to their frequency of observation and isobaric tag for relative and absolute quantitation (iTRAQ) reporter ion quality. Retention times of selected peptides were aligned using similarity driven pairwise alignment strategy yielding <1 min standard deviation for 4 h gradients. Multiple fragmentation of the same peptides resulted in better statistics and more precise reporter ion based quantification without any loss in coverage. Overall, 24% more target proteins were quantified using the targeted data acquisition approach, and precision of quantification improved by >1.5-fold. We also show that a combination of higher energy collisional dissociation (HCD) with collisional induced dissociation (CID) outperformed pulsed-Q-dissociation (PQD) on the OrbitrapXL. With the CID/ HCD based targeted data acquisition approach 10% more quantifiable target proteins were identified and a 2-fold increase in quantification precision was achieved. We have observed excellent reproducibility between different instruments, underlining the robustness of the approach.     

Identification of Proteins and Phosphoproteins Using Pulsed Q Collision Induced Dissociation (PQD)

Pulsed Q collision induced dissociation (PQD) was developed to facilitate detection of low-mass reporter ions from labeling reagents (e.g., iTRΑQ) in peptide quantification using an LTQ mass spectrometer (MS). Despite the large number of linear ion traps worldwide, the use and optimization of PQD for protein identification have been limited, in part due to less effective ion fragmentation relative to the collision induced dissociation (CID). PQD expands the m/z coverage of fragment ions to the lower m/z range by circumventing the typical low mass cut-off of an ion trap MS. Since database searching relies on the matching between theoretical and observed spectra, it is not clear how ion intensity and peak number might affect the outcomes of a database search. In this report, we systematically evaluated the attributes of PQD mass spectra, performed intensity optimization, and assessed the benefits of using PQD on the identification of peptides and phosphopeptides from an LTQ. Based on head-to-head comparisons between CID (higher intensity) and PQD (better m/z coverage), peptides identified using PQD generally have Xcorr scores lower than those using CID. Such score differences were considerably diminished by the use of 0.1% m-nitrobenzyl alcohol (m-NBA) in mobile phases. The ion intensities of both CID and PQD were adversely affected by increasing m/z of the precursor, with PQD more sensitive than CID. In addition to negating the 1/3 rule, PQD enhances direct bond cleavage and generates patterns of fragment ions different from those of CID, particularly for peptides with a labile functional group (e.g., phosphopeptides). The higher energy fragmentation pathway of PQD on peptide fragmentation was further compared to those of CID and the quadrupole-type activation in parallel experiments.     

Characterizing protein glycosylation sites through higher‐energy C‐trap dissociation

Assigning glycosylation sites of glycoproteins and their microheterogeneity is still a very challenging analytical task despite the rapid advancements in mass spectrometry. It is shown here that glycopeptide ions can be fragmented efficiently using the higher‐energy C‐trap dissociation (HCD) feature of a linear ion trap orbitrap hybrid mass spectrometer (LTQ Orbitrap). An attractive aspect of this dissociation option is the generation of distinct Y1 ions (peptide+GlcNAc), thus allowing unequivocal assignment of N‐glycosylation sites of glycoproteins. The combination of the very informative collision‐induced dissociation spectra acquired in the linear ion trap with the distinct features of HCD offers very useful information aiding in the characterization of the glycosylation sites of glycoproteins. The HCD activation energy needed to obtain optimum Y1 ions was studied in terms of glycan structure and charge state, and size and structure of the peptide backbone. The latter appeared to be primarily dictating the needed HCD energy. The distinct Y1 ion formation in HCD facilitated an easy assignment of such an ion and its subsequent isolation and dissociation through multiple‐stage tandem mass spectrometry. The resulting MS³ spectrum of the Y1 ion facilitates database searching and de novo sequencing thus prompting the subsequent identification of the peptide backbone and associated glycosylation sites. Moreover, fragment ions formed by HCD are detected in the Orbitrap, thus overcoming the 1/3 cut‐off limitation that is commonly associated with ion trap mass spectrometers. As a result, in addition to the Y1 ion, the common glycan oxonium ions are also detected. The high mass accuracy offered by the LTQ Orbitrap mass spectrometer is also an attractive feature that allows a confident assignment of protein glycosylation sites and the microheterogeneity of such sites. Copyright © 2010 John Wiley & Sons, Ltd.     

Transmission mode ion/ion reactions in the radiofrequency‐only ion guide of hybrid tandem mass spectrometers

Transmission mode ion/ion reactions have been performed within the first quadrupole, the Q0 radiofrequency (RF)‐only quadrupole, of two types of hybrid tandem mass spectrometers (viz., triple quadrupole/linear ion trap and QqTOF instruments). These transmission mode reactions involved the storage of either the reagent species and the transmission of the analyte species through the Q0 quadrupole for charge inversion reactions or the storage of the analyte ions and transmission of the reagent ions as in charge reduction experiments. A key advantage to the use of transmission mode ion/ion reactions is that they do not require any instrument hardware modifications to provide interactions of oppositely charged ions and can be implemented in any instrument that contains a quadrupole or linear ion trap. The focus of this work was to investigate the potential of using the RF‐only quadrupole ion guide positioned prior to the first mass‐resolving element in a tandem mass spectrometer for ion/ion reactions. Two types of exemplary experiments have been demonstrated. One involved a charge inversion reaction and the other involved a charge reduction reaction in conjunction with ion parking. Ion/ion reactions proved to be readily implemented in Q0 thereby adding significantly greater experimental flexibility in the use of ion/ion reaction experiments with hybrid tandem mass spectrometers. Copyright © 2009 John Wiley & Sons, Ltd.     

The Multicomponent Hantzsch Reaction: Comprehensive Mass Spectrometry Monitoring Using Charge‐Tagged Reagents

A novel strategy for the ESI‐MS monitoring of reaction solutions involving the alternate use of permanently charge‐tagged reagents has been used for comprehensive mass spectrometry monitoring of the multicomponent Hantzsch 1,4‐dihydropyridine reaction. By placing a charge tag on either, or both, of the two key reactants, ion suppression effects for ESI were eliminated or minimized, and comprehensive detection of charge‐tagged intermediates was achieved. The strategy allowed the trapping and characterization of the important intermediates in the mechanism for 1,4‐dihydropyridine formation.     

Optimization of a quadrupole ion storage trap as a source for time‐of‐flight mass spectrometry

Designs of a quadrupole ion trap (QIT) as a source for time‐of‐flight (TOF) mass spectrometry are evaluated for mass resolution, ion trapping, and laser activation of trapped ions. Comparisons are made with the standard hyperbolic electrode ion trap geometry for TOF mass analysis in both linear and reflectron modes. A parallel‐plate design for the QIT is found to give significantly improved TOF mass spectrometer performance. Effects of ion temperature, trapped ion cloud size, mass, and extraction field on mass resolution are investigated in detail by simulation of the TOF peak profiles. Mass resolution (m/Δm) values of several thousand are predicted even at room temperature with moderate extraction fields for the optimized design. The optimized design also allows larger radial ion collection size compared with the hyperbolic ion trap, without compromising the mass resolution. The proposed design of the QIT also improves the ion–laser interaction volume and photon collection efficiency for fluorescence measurements on trapped ions. Copyright © 2011 John Wiley & Sons, Ltd.     

A mass spectrometric method for rapidly assaying the chiral selectivities of the copper(I) complexes of C2‐symmetric ligands

A gas‐phase method for rapidly assaying the enantioselectivity of metal‐centered catalysts is presented. It relies on gas‐phase equilibrium measurements in a quadrupole ion trap mass spectrometer. A group of well‐established C₂‐symmetric bis‐oxazoline copper(I) complexes was used to identify chiral probe reagents that are capable of profiling the quality of the asymmetric environment provided by the metal complex. The chiral probes were then applied to a wide variety of copper(I) bis‐di‐imine complexes. Complexes based on a BINAM backbone exhibited selectivities that were comparable to the bis‐oxazolines. Taking advantage of the mass selectivity capabilities of the ion trap mass spectrometer, the method was also applied to an un‐purified mix of copper(I) complexes derived from a combinatorial synthesis of bis‐di‐imine ligands. This approach holds promise as a rapid screening tool for potential chiral catalysts. Copyright © 2015 John Wiley & Sons, Ltd.     

负热电离质谱测定硼同位素的涂样试剂比较

目前人们并未注意到利用负热电离质谱方法测定硼同位素所采用涂样试剂中BO^-的同质异位素CNO^-离子的存在和影响。对硼同位素测定采用的不同涂样试剂进行比较，结果发现在去硼海水和硝酸盐溶液中存在BO2^-的同质异位素CNO^-离子，干扰离子不仅来自有机物，而且可能来自硝酸根。在硼同位素测定中，检查空白中的43峰和43／42比值是必要的。实验表明MgCl2 NaOH混合溶液是负热电离质谱测定硼同位素的较为理想的涂样试剂。     

Elucidation of the dissociation pathways of electro‐ionized estrone

With the future aim of using gas chromatography coupled with mass spectrometry to characterize the transformation products of estrone submitted to UV‐photolysis or to waste water treatment plants, an interpretation of the electron impact mass spectrum of estrone is presented. Fragmentation mechanisms are proposed on the basis of high‐resolution measurements performed with a magnetic sector analyzer. Multiple‐stage mass spectrometry experiments were carried out using an ion trap mass spectrometer. The structures proposed for product ions were confirmed by the m/z shifts observed in the estrone‐d₄ and estrone methyl ether electron ionization mass spectra. If the formation of some of the most abundant ions may easily be explained by α‐cleavages and retro‐Diels‐Alder type rearrangements, complex mechanisms need to be considered to rationalize the formation of others. Isotope labelling allows discrimination of isobaric ions. Copyright © 2010 John Wiley & Sons, Ltd.     

On the inter‐instrument and inter‐laboratory transferability of a tandem mass spectral reference library: 1. Results of an Austrian multicenter study

The inter‐instrument and inter‐laboratory transferability of a tandem mass spectral reference library originally built on a quadrupole‐quadrupole‐time‐of‐flight instrument was examined. The library consisted of 3759 MS/MS spectra collected from 402 reference compounds applying several different collision‐energy values for fragmentation. In the course of the multicenter study, 22 test compounds were sent to three different laboratories, where 418 tandem mass spectra were acquired using four different instruments from two manufacturers. The study covered the following types of tandem mass spectrometers: quadrupole‐quadrupole‐time‐of‐flight, quadrupole‐quadrupole‐linear ion trap, quadrupole‐quadrupole‐quadrupole, and linear ion trap‐Fourier transform ion cyclotron resonance mass spectrometer. In each participating laboratory, optimized instrumental parameters were gathered solely from routinely applied workflows. No standardization procedure was applied to increase the inter‐instrument comparability of MS/MS spectra. The acquired tandem mass spectra were matched against the established reference library using a sophisticated matching algorithm, which is presented in detail in a companion paper. Correct answers, meaning that the correct compound was retrieved as top hit, were obtained in 98.1% of cases. For the remaining 1.9% of spectra, the correct compound was matched at second rank. The observed high percentage of correct assignments clearly suggests that the developed mass spectral library search approach is to a large extent platform independent. Copyright © 2009 John Wiley & Sons, Ltd.     

Synthesis of biotin‐tagged chemical cross‐linkers and their applications for mass spectrometry

Chemical cross‐linking combined with mass spectrometry (MS) has been used to elucidate protein structures and protein‐protein interactions. However, heterogeneity of the samples and the relatively low abundance of cross‐linked peptides make this approach challenging. As an effort to overcome this hurdle, we have synthesized lysine‐reactive homobifunctional cross‐linkers with the biotin in the middle of the linker and used them to enrich cross‐linked peptides. The reaction of biotin‐tagged cross‐linkers with purified HIV‐1 CA resulted in the formation of hanging and intramolecular cross‐links. The peptides modified with biotinylated cross‐linkers were effectively enriched and recovered using a streptavidin‐coated plate and MS‐friendly buffers. The enrichment of modified peptides and removal of the dominantly unmodified peptides simplify mass spectra and their analyses. The combination of the high mass accuracy of Fourier transform ion cyclotron resonance (FT‐ICR) MS and the tandem mass spectrometric (MS/MS) capability of the linear ion trap allows us to unambiguously identify the cross‐linking sites and additional modification, such as oxidation. Copyright © 2009 John Wiley & Sons, Ltd.     

Does the reagent gas influence collisional activation when performing in situ chemical ionization with an ion trap mass spectrometer?

Users of ion trap mass spectrometers frequently develop methods that associate chemical ionization with tandem mass spectrometry detection. With apparatus using internal ionization, the chemical reagent is present in the trap during the collision induced dissociation (CID) step and one may wonder if the reagent influences the fragmentation ratios in MS/MS. We report a comparison of the fragmentation ratios of protonated molecules when using the most common reagents (methane, ammonia, methanol, acetonitrile, isobutane) for performing in situ chemical ionization. Four molecules were chosen in the medical field to serve as models: alprazolam, diazepam, flunitrazepam and acetaminophen. In the non-resonant CID mode, the influence of the reagent mass is clearly seen in spite of its low partial pressure in the ion trap; the reagent acts as a "heavy target": the degree of fragmentation increases with the molecular weight of the reagent. In the resonant CID mode, there is no evident correlation between the fragmentation ratio of MH(+) ions and the nature of the CI reagent; a slight shift of the secular frequency of the precursor ion, which tends to reduce the CID efficiency, could compensate for the "heavy target" effect underscored in the non-resonant mode.     

Direct sampling and analysis from solid-phase extraction cards using an automated liquid extraction surface analysis nanoelectrospray mass spectrometry system

Direct liquid extraction based surface sampling, a technique previously demonstrated with continuous flow and autonomous pipette liquid microjunction surface sampling probes, has recently been implemented as a liquid extraction surface analysis (LESA) mode on a commercially available chip‐based infusion nanoelectrospray ionization (nanoESI) system. In the present paper, the LESA mode was applied to the analysis of 96‐well format custom‐made solid‐phase extraction (SPE) cards, with each well consisting of either a 1 or a 2 mm diameter monolithic hydrophobic stationary phase. These substrate wells were conditioned, loaded with either single or multi‐component aqueous mixtures, and read out using the commercial nanoESI system coupled to a hybrid triple quadrupole/linear ion trap mass spectrometer or a linear ion trap mass spectrometer. The extraction conditions, including extraction/nanoESI solvent composition, volume, and dwell times, were optimized in the analysis of targeted compounds. Limit of detection and quantitation as well as analysis reproducibility figures of merit were measured. Calibration data was obtained for propranolol using a deuterated internal standard which demonstrated linearity and reproducibility. A 10× increase in signal and cleanup of micromolar angiotensin II from a concentrated salt solution was demonstrated. In addition, a multicomponent herbicide mixture at ppb concentration levels was analyzed using MS³ spectra for compound identification in the presence of isobaric interferences. Published in 2011 by John Wiley & Sons, Ltd.